Mutagenetix > Incidental Mutation

Incidental Mutation 'R0426:Ddx39a'

38656

Institutional Source

Beutler Lab

Gene Symbol

Ddx39a

Ensembl Gene

ENSMUSG00000005481

Gene Name

DEAD box helicase 39a

Synonyms

BAT1, 2610307C23Rik, Ddx39

MMRRC Submission

038628-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.940) question?

Stock #

R0426 (G1)

Quality Score

224

Status

Validated

Chromosome

Chromosomal Location

84441806-84453521 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 84448398 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 217 (T217A)

Ref Sequence

ENSEMBL: ENSMUSP00000148329 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002964] [ENSMUST00000019576] [ENSMUST00000075843] [ENSMUST00000109802] [ENSMUST00000109810] [ENSMUST00000172396] [ENSMUST00000212949] [ENSMUST00000166939] [ENSMUST00000140521]

AlphaFold

Q8VDW0

Predicted Effect

probably benign
Transcript: ENSMUST00000002964

SMART Domains

Protein: ENSMUSP00000002964
Gene: ENSMUSG00000002885

Domain	Start	End	E-Value	Type
EGF	30	68	1.63e1	SMART
EGF_CA	69	119	5.92e-8	SMART
EGF_CA	120	167	1.78e-11	SMART
GPS	384	430	2.18e-8	SMART
Pfam:Dicty_CAR	431	703	1.3e-8	PFAM
Pfam:7tm_2	432	672	8.1e-68	PFAM
low complexity region	704	714	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000019576
AA Change: T217A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000019576
Gene: ENSMUSG00000005481
AA Change: T217A

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	264	4.06e-54	SMART
HELICc	300	381	9.09e-25	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000075843

SMART Domains

Protein: ENSMUSP00000075240
Gene: ENSMUSG00000002885

Domain	Start	End	E-Value	Type
EGF	30	68	1.63e1	SMART
EGF_CA	69	119	5.92e-8	SMART
EGF_CA	165	213	1.38e-8	SMART
EGF_CA	214	261	1.78e-11	SMART
GPS	478	524	2.18e-8	SMART
Pfam:Dicty_CAR	525	798	4.6e-8	PFAM
Pfam:7tm_2	526	766	5.3e-68	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000109802

SMART Domains

Protein: ENSMUSP00000105427
Gene: ENSMUSG00000002885

Domain	Start	End	E-Value	Type
EGF	30	68	1.63e1	SMART
EGF_CA	69	119	5.92e-8	SMART
EGF_CA	120	168	1.38e-8	SMART
EGF_CA	169	216	1.78e-11	SMART
GPS	433	479	2.18e-8	SMART
Pfam:Dicty_CAR	480	752	5.3e-8	PFAM
Pfam:7tm_2	481	721	7.5e-67	PFAM
low complexity region	753	763	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000109810
AA Change: T217A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000105435
Gene: ENSMUSG00000005481
AA Change: T217A

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	264	4.06e-54	SMART
HELICc	300	381	9.09e-25	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127505

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138789

Predicted Effect

probably benign
Transcript: ENSMUST00000172396
AA Change: T217A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000132222
Gene: ENSMUSG00000005481
AA Change: T217A

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	264	4.06e-54	SMART
HELICc	300	381	9.09e-25	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000212949
AA Change: T217A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139797

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140606

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184114

Predicted Effect

probably benign
Transcript: ENSMUST00000166939

SMART Domains

Protein: ENSMUSP00000128220
Gene: ENSMUSG00000002885

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
EGF	28	66	1.63e1	SMART
EGF_CA	67	117	5.92e-8	SMART
EGF_CA	118	165	1.78e-11	SMART
GPS	382	428	2.18e-8	SMART
Pfam:Dicty_CAR	429	701	2.1e-7	PFAM
Pfam:7tm_2	430	670	1.7e-66	PFAM
low complexity region	702	712	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000140521

SMART Domains

Protein: ENSMUSP00000116101
Gene: ENSMUSG00000005481

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	208	2.82e-21	SMART

Meta Mutation Damage Score

0.2331

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

96% (86/90)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the DEAD box protein family. These proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is thought to play a role in the prognosis of patients with gastrointestinal stromal tumors. A pseudogene of this gene is present on chromosome 13. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	G	T	11: 109,845,853 (GRCm39)		probably benign	Het
Acadl	A	T	1: 66,880,805 (GRCm39)	F320L	probably damaging	Het
Acsbg1	T	C	9: 54,530,030 (GRCm39)	D222G	probably benign	Het
Anapc15	A	G	7: 101,547,240 (GRCm39)	T39A	probably benign	Het
Ano3	A	T	2: 110,491,519 (GRCm39)	V919E	probably damaging	Het
Arhgef12	T	C	9: 42,882,286 (GRCm39)		probably null	Het
Atad5	T	A	11: 80,003,658 (GRCm39)	I1091N	probably benign	Het
Atf1	A	T	15: 100,130,708 (GRCm39)	H26L	possibly damaging	Het
Atp10a	T	C	7: 58,434,482 (GRCm39)	M252T	probably benign	Het
Btbd8	C	T	5: 107,658,239 (GRCm39)	T1603I	probably damaging	Het
Cd55	C	T	1: 130,376,109 (GRCm39)	R347H	probably benign	Het
Cdc27	A	C	11: 104,403,853 (GRCm39)		probably null	Het
Cdh9	G	A	15: 16,823,540 (GRCm39)		probably null	Het
Cdk11b	T	C	4: 155,726,969 (GRCm39)		probably benign	Het
Cep70	A	G	9: 99,179,737 (GRCm39)	D567G	probably benign	Het
Cep78	A	T	19: 15,948,334 (GRCm39)	Y382*	probably null	Het
Cgas	G	A	9: 78,343,020 (GRCm39)		probably benign	Het
Col9a2	T	C	4: 120,901,857 (GRCm39)		probably benign	Het
Cyp2d12	G	A	15: 82,443,164 (GRCm39)	D409N	probably benign	Het
Dennd1b	T	A	1: 139,097,934 (GRCm39)	D733E	probably benign	Het
Dicer1	A	G	12: 104,668,801 (GRCm39)	S1294P	probably damaging	Het
Dnah3	T	C	7: 119,542,795 (GRCm39)	E3539G	probably benign	Het
Dnmbp	A	G	19: 43,840,875 (GRCm39)		probably benign	Het
Dysf	T	C	6: 84,126,739 (GRCm39)	L1332P	probably damaging	Het
F5	A	G	1: 164,010,409 (GRCm39)	D380G	probably damaging	Het
Fam171a1	T	C	2: 3,226,433 (GRCm39)	V522A	probably benign	Het
Fhip1b	A	C	7: 105,038,680 (GRCm39)	C186W	probably damaging	Het
Galr2	C	A	11: 116,172,517 (GRCm39)	A69D	probably damaging	Het
Grk2	T	C	19: 4,340,628 (GRCm39)		probably null	Het
Gtf3c1	A	T	7: 125,262,188 (GRCm39)	Y1119*	probably null	Het
Hgd	A	T	16: 37,409,047 (GRCm39)		probably benign	Het
Ildr2	G	T	1: 166,136,468 (GRCm39)	V436L	probably benign	Het
Intu	G	A	3: 40,629,735 (GRCm39)	C355Y	probably damaging	Het
Irf2bpl	G	T	12: 86,929,870 (GRCm39)	P268T	probably benign	Het
Jarid2	T	C	13: 44,994,358 (GRCm39)		probably null	Het
Jup	A	T	11: 100,263,227 (GRCm39)	M716K	probably benign	Het
Kank1	G	A	19: 25,388,837 (GRCm39)	V809I	probably damaging	Het
Kdm1b	T	A	13: 47,217,720 (GRCm39)		probably benign	Het
Kdm3a	C	T	6: 71,577,739 (GRCm39)	C687Y	probably damaging	Het
Kdm5d	T	A	Y: 942,437 (GRCm39)		probably benign	Het
Kifap3	T	A	1: 163,693,121 (GRCm39)		probably benign	Het
Macf1	T	A	4: 123,377,453 (GRCm39)	K1400*	probably null	Het
Majin	A	G	19: 6,262,147 (GRCm39)		probably benign	Het
Mctp1	A	G	13: 77,168,940 (GRCm39)	I846V	probably benign	Het
Mrgpra2b	T	A	7: 47,113,875 (GRCm39)	I286F	possibly damaging	Het
Neil3	T	G	8: 54,062,431 (GRCm39)		probably benign	Het
Nox3	G	T	17: 3,745,838 (GRCm39)	N23K	probably damaging	Het
Nt5c3	T	C	6: 56,860,797 (GRCm39)	K219E	probably benign	Het
Or1e29	T	A	11: 73,667,263 (GRCm39)	M297L	probably benign	Het
Or52b4i	T	A	7: 102,191,893 (GRCm39)	I250N	probably damaging	Het
Or5b105	G	A	19: 13,080,642 (GRCm39)	R3C	possibly damaging	Het
Or6b13	A	C	7: 139,782,029 (GRCm39)	F218C	possibly damaging	Het
Or6d13	A	T	6: 116,517,446 (GRCm39)	N11Y	probably damaging	Het
Or8g34	T	C	9: 39,372,889 (GRCm39)	L54P	probably damaging	Het
Pacsin2	A	G	15: 83,263,996 (GRCm39)	V347A	possibly damaging	Het
Pcdhb7	A	T	18: 37,475,857 (GRCm39)	E331V	probably damaging	Het
Pcid2	A	C	8: 13,131,262 (GRCm39)		probably null	Het
Pcsk9	T	C	4: 106,307,274 (GRCm39)	D323G	possibly damaging	Het
Pdhb	T	C	14: 8,169,801 (GRCm38)	E203G	probably damaging	Het
Phlpp2	A	G	8: 110,655,095 (GRCm39)	Y630C	probably benign	Het
Pidd1	C	T	7: 141,019,046 (GRCm39)	A812T	probably damaging	Het
Plau	G	A	14: 20,892,382 (GRCm39)	R389H	probably benign	Het
Plekhg6	G	A	6: 125,341,592 (GRCm39)		probably null	Het
Ppox	T	C	1: 171,105,322 (GRCm39)	Y321C	probably damaging	Het
Pxdn	A	G	12: 30,037,065 (GRCm39)	N281S	possibly damaging	Het
Pycr3	A	T	15: 75,790,237 (GRCm39)	M138K	probably benign	Het
Radil	T	C	5: 142,483,628 (GRCm39)	Y526C	probably damaging	Het
Ranbp3	C	A	17: 57,014,169 (GRCm39)	D233E	probably benign	Het
Rhpn1	A	G	15: 75,583,721 (GRCm39)	Q402R	possibly damaging	Het
Sec23b	T	A	2: 144,410,532 (GRCm39)		probably benign	Het
Sel1l2	A	T	2: 140,082,832 (GRCm39)	L602*	probably null	Het
Sema5b	G	A	16: 35,466,725 (GRCm39)	G209D	probably damaging	Het
Svep1	T	C	4: 58,073,333 (GRCm39)	Y1992C	possibly damaging	Het
Syncrip	T	A	9: 88,338,312 (GRCm39)		probably benign	Het
Synj1	G	T	16: 90,764,242 (GRCm39)	A65E	probably damaging	Het
Taar2	G	A	10: 23,817,393 (GRCm39)	R311H	probably benign	Het
Tecrl	T	C	5: 83,502,610 (GRCm39)		probably benign	Het
Tenm4	G	T	7: 96,427,058 (GRCm39)	G698C	probably damaging	Het
Tmem209	G	A	6: 30,491,181 (GRCm39)	L259F	probably damaging	Het
Tmem247	G	A	17: 87,225,931 (GRCm39)	E124K	possibly damaging	Het
Tnks2	C	A	19: 36,830,221 (GRCm39)	A218E	probably damaging	Het
Tppp	T	A	13: 74,169,430 (GRCm39)	F57I	probably damaging	Het
Trim36	A	G	18: 46,305,592 (GRCm39)	W452R	probably damaging	Het
Vars2	A	T	17: 35,975,476 (GRCm39)	V262E	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Zfp516	G	T	18: 82,973,897 (GRCm39)	A32S	probably benign	Het
Zfy2	G	T	Y: 2,107,348 (GRCm39)	L429I	possibly damaging	Het

Other mutations in Ddx39a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02544:Ddx39a	APN	8	84,449,402 (GRCm39)	missense	probably benign	0.03
IGL02712:Ddx39a	APN	8	84,448,386 (GRCm39)	missense	probably benign	0.03
R0038:Ddx39a	UTSW	8	84,449,127 (GRCm39)	missense	probably damaging	1.00
R0038:Ddx39a	UTSW	8	84,449,127 (GRCm39)	missense	probably damaging	1.00
R0051:Ddx39a	UTSW	8	84,447,251 (GRCm39)	missense	possibly damaging	0.83
R0051:Ddx39a	UTSW	8	84,447,251 (GRCm39)	missense	possibly damaging	0.83
R0143:Ddx39a	UTSW	8	84,447,179 (GRCm39)	missense	probably benign	0.22
R0147:Ddx39a	UTSW	8	84,449,105 (GRCm39)	missense	possibly damaging	0.74
R0148:Ddx39a	UTSW	8	84,449,105 (GRCm39)	missense	possibly damaging	0.74
R0392:Ddx39a	UTSW	8	84,448,366 (GRCm39)	missense	probably damaging	0.97
R0830:Ddx39a	UTSW	8	84,446,452 (GRCm39)	missense	possibly damaging	0.47
R1509:Ddx39a	UTSW	8	84,446,527 (GRCm39)	missense	probably damaging	1.00
R2935:Ddx39a	UTSW	8	84,447,587 (GRCm39)	missense	possibly damaging	0.57
R3082:Ddx39a	UTSW	8	84,449,335 (GRCm39)	missense	possibly damaging	0.57
R4050:Ddx39a	UTSW	8	84,448,863 (GRCm39)	missense	probably benign	0.00
R4647:Ddx39a	UTSW	8	84,448,902 (GRCm39)	missense	probably benign	0.00
R4804:Ddx39a	UTSW	8	84,447,724 (GRCm39)	missense	probably damaging	0.99
R5242:Ddx39a	UTSW	8	84,448,440 (GRCm39)	missense	probably benign	0.01
R5268:Ddx39a	UTSW	8	84,448,950 (GRCm39)	missense	probably benign	0.08
R6598:Ddx39a	UTSW	8	84,449,556 (GRCm39)	missense	probably benign	0.03
R6805:Ddx39a	UTSW	8	84,449,766 (GRCm39)	missense	probably damaging	1.00
R6852:Ddx39a	UTSW	8	84,449,646 (GRCm39)	missense	probably benign	0.03
R7326:Ddx39a	UTSW	8	84,449,100 (GRCm39)	missense	probably benign	0.31
R7559:Ddx39a	UTSW	8	84,447,595 (GRCm39)	missense	possibly damaging	0.82
R7803:Ddx39a	UTSW	8	84,446,229 (GRCm39)	critical splice donor site	probably null
R8103:Ddx39a	UTSW	8	84,451,105 (GRCm39)	critical splice acceptor site	probably null
R9187:Ddx39a	UTSW	8	84,449,113 (GRCm39)	missense	probably benign
R9483:Ddx39a	UTSW	8	84,448,916 (GRCm39)	missense	probably benign	0.14
R9631:Ddx39a	UTSW	8	84,447,729 (GRCm39)	missense	possibly damaging	0.92
X0026:Ddx39a	UTSW	8	84,448,959 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- TTTCCTGAAGCGTGGCTCAAGG -3'
(R):5'- AAAGCCGGATGTAAGCTCTGCCTC -3'

Sequencing Primer
(F):5'- AGTAAGTGGACCGCAGCTC -3'
(R):5'- TCAGGTGTGGACCACTCAG -3'

Posted On

2013-05-23